nirs4all package

Subpackages

• nirs4all.analysis package
  • Submodules
    • nirs4all.analysis.playground_dataset module
      • PlaygroundDatasetSelection
      • extract_playground_dataset()
      • playground_metadata_columns()
    • nirs4all.analysis.playground_distances module
      • paired_spectral_distances()
      • repetition_variance()
    • nirs4all.analysis.playground_execution module
      • execute_preview()
    • nirs4all.analysis.playground_facade module
      • preview_arrays()
      • preview_spectro_dataset()
    • nirs4all.analysis.playground_metrics module
      • descriptor_statistics()
    • nirs4all.analysis.playground_partition module
    • nirs4all.analysis.playground_prepare module
    • nirs4all.analysis.playground_projections module
    • nirs4all.analysis.playground_statistics module
    • nirs4all.analysis.playground_steps module
    • nirs4all.analysis.playground_types module
    • nirs4all.analysis.presets module
      • get_preset()
      • list_presets()
    • nirs4all.analysis.projections module
    • nirs4all.analysis.results module
      • TransferResult
      • TransferSelectionResults
    • nirs4all.analysis.selector module
      • TransferPreprocessingSelector
    • nirs4all.analysis.transfer_metrics module
    • nirs4all.analysis.transfer_utils module
      • apply_single_preprocessing()
      • generate_object_augmentation_combinations()
      • generate_object_stacked_pipelines()
      • generate_stacked_pipelines()
      • normalize_preprocessing_list()
• nirs4all.api package
  • Submodules
    • nirs4all.api.advanced_capabilities module
      • AdvancedApiCapabilityDecision
      • advanced_api_capability_ledger()
      • preflight_advanced_api()
    • nirs4all.api.calibrate module
      • ConformalCalibrationData
      • Nirs4AllCalibrationNotImplementedError
      • attach_calibrated_result_to_bundle()
      • calibrate()
      • conformal_metrics()
      • export_calibrated_result()
      • load_calibrated_result()
      • load_workspace_calibrated_predict_result()
      • load_workspace_calibrated_result()
      • predict_calibrated()
      • save_workspace_calibrated_result()
    • nirs4all.api.dagml_training module
      • execute_training()
      • run_host_hpo_search()
    • nirs4all.api.dataset_documents module
      • DatasetDocumentLimits
      • normalize_dataset_document()
    • nirs4all.api.dataset_inspection module
      • dataset_statistics()
      • inspect_format_file()
      • load_dataset_for_analysis()
      • load_prediction_file()
      • preview_dataset()
    • nirs4all.api.explain module
      • explain()
      • explain_preflight()
    • nirs4all.api.general_explain module
      • explain_general()
    • nirs4all.api.general_retrain module
      • captured_training_spec()
    • nirs4all.api.general_synthesis module
      • studio_synthetic_dataset_job_v1()
    • nirs4all.api.general_transfer module
      • BoundTransferOperator
      • FrozenTransferTransform
      • bind_transfer_operators()
      • fresh_training_estimator()
      • transfer_training_steps()
    • nirs4all.api.generate module
      • builder()
      • category()
      • classification()
      • from_template()
      • generate()
      • generate_preflight()
      • multi_source()
      • product()
      • regression()
      • to_csv()
      • to_folder()
    • nirs4all.api.inspector_json module
      • sanitize_dict()
      • sanitize_float()
    • nirs4all.api.inspector_normalization module
    • nirs4all.api.inspector_views module
      • BiasVarianceEntry
      • BiasVarianceRequest
      • BiasVarianceResponse
      • BranchComparisonEntry
      • BranchComparisonRequest
      • BranchComparisonResponse
      • BranchTopologyResponse
      • CandlestickCategory
      • CandlestickRequest
      • CandlestickResponse
      • ConfusionMatrixCell
      • ConfusionMatrixRequest
      • ConfusionMatrixResponse
      • FoldScoreEntry
      • FoldStabilityRequest
      • FoldStabilityResponse
      • HeatmapCell
      • HeatmapRequest
      • HeatmapResponse
      • HistogramBin
      • HistogramResponse
      • HyperparameterPoint
      • HyperparameterRequest
      • HyperparameterResponse
      • InspectorDataResponse
      • InspectorViewError
      • PreprocessingImpactEntry
      • PreprocessingImpactRequest
      • PreprocessingImpactResponse
      • RankingsResponse
      • ScatterPoint
      • ScatterRequest
      • ScatterResponse
      • ScoreRef
      • TopologyNode
      • get_bias_variance()
      • get_branch_comparison()
      • get_branch_topology()
      • get_candlestick_data()
      • get_confusion_matrix()
      • get_fold_stability()
      • get_heatmap_data()
      • get_histogram_data()
      • get_hyperparameter_data()
      • get_inspector_data()
      • get_preprocessing_impact()
      • get_rankings_data()
      • get_scatter_data()
      • read_inspector_view()
    • nirs4all.api.library_playground module
      • studio_playground_job_v1()
    • nirs4all.api.native_archive_training module
      • NativeArchiveTrainingError
      • NativeMethodsArchiveRunResult
      • NativeMethodsHpoCapabilityError
      • run_native_methods_archive()
    • nirs4all.api.native_capabilities module
      • get_native_capability_matrix()
      • native_capability_matrix_schema()
      • validate_native_capability_matrix()
    • nirs4all.api.native_refit_result module
      • NativeMethodsRefitResult
    • nirs4all.api.native_result module
      • NativeMethodsRunResult
    • nirs4all.api.native_retrain_lineage module
      • NativeRetrainLineage
    • nirs4all.api.native_session module
      • NativeMethodsSession
    • nirs4all.api.native_training module
      • fit_native_pipeline()
      • run_native_methods()
    • nirs4all.api.native_witness module
      • NativeMethodsExecutionClaim
      • NativeMethodsTerminalExecutionClaim
    • nirs4all.api.portable_archive module
      • inspect_portable_predictor_archive_v2()
      • read_portable_predictor_archive_v2()
      • replay_portable_predictor_archive_v2()
      • write_portable_predictor_archive_v2()
    • nirs4all.api.predict module
      • predict()
    • nirs4all.api.public_results module
      • open_experiment()
      • save_experiment()
    • nirs4all.api.public_tuning module
      • generate_variants()
      • load_native_tuning()
      • resume_native_tuning()
      • tune_native()
    • nirs4all.api.result module
      • LazyModelRefitResult
      • ModelRefitResult
      • load_workspace_predict_result()
      • load_workspace_predict_results()
      • save_workspace_predict_result()
    • nirs4all.api.retrain module
      • retrain()
      • retrain_preflight()
    • nirs4all.api.retrain_capabilities module
      • retrain_capability_ledger()
    • nirs4all.api.robustness module
      • RobustnessMetricSet
      • RobustnessReport
      • RobustnessScenarioResult
      • RobustnessScenarioSpec
      • RobustnessSliceResult
      • get_robustness_summary_schema()
      • load_workspace_robustness_report()
      • robustness()
      • robustness_summary_schema_json()
      • save_workspace_robustness_report()
    • nirs4all.api.run module
      • run()
    • nirs4all.api.run_selection module
      • select_run_engine()
    • nirs4all.api.session module
      • SessionClosedError
      • load_native_archive_session()
      • load_session()
      • session()
    • nirs4all.api.studio_lineage module
      • reconcile_studio_job_lineage()
      • record_studio_run_provenance()
      • recover_studio_job_lineage()
      • validate_studio_provenance()
    • nirs4all.api.studio_scientific module
      • studio_scientific_job_v1()
    • nirs4all.api.studio_scientific_general module
      • studio_scientific_job_v2()
      • validate_studio_pipeline_config()
    • nirs4all.api.tuning module
      • NativeTuning
      • OrderedSearchSpaceSpec
      • ParameterPatch
      • SearchSpaceParameter
      • TunedSingleEstimatorConformalResult
      • TuningCalibration
      • TuningConformalScoreCalibration
      • TuningPassthrough
      • TuningScoreData
      • TuningWinner
      • get_tuning_space_schema()
      • inspect_tuning_space()
      • load_workspace_tuning_result()
      • save_workspace_tuning_result()
      • tune_single_estimator()
      • tuning_space_schema_json()
    • nirs4all.api.workspace_chain_snapshot module
      • workspace_chain_snapshot()
• nirs4all.cli package
  • Subpackages
    • nirs4all.cli.commands package
      • Submodules
  • Submodules
    • nirs4all.cli.installation_test module
      • check_dependency()
      • test_installation()
      • test_integration()
    • nirs4all.cli.main module
      • get_version()
      • main()
• nirs4all.config package
  • Submodules
    • nirs4all.config.cache_config module
    • nirs4all.config.validator module
      • ConfigValidationError
      • get_validation_summary()
      • validate_config_file()
      • validate_dataset_config()
      • validate_pipeline_config()
• nirs4all.controllers package
  • Subpackages
    • nirs4all.controllers.charts package
      • Submodules
    • nirs4all.controllers.data package
      • Submodules
    • nirs4all.controllers.flow package
      • Submodules
    • nirs4all.controllers.models package
      • Subpackages
      • Submodules
    • nirs4all.controllers.shared package
      • Submodules
    • nirs4all.controllers.splitters package
      • Submodules
    • nirs4all.controllers.transforms package
      • Submodules
  • Submodules
    • nirs4all.controllers.base module
      • BaseController
    • nirs4all.controllers.controller module
    • nirs4all.controllers.presets module
    • nirs4all.controllers.registry module
      • reset_registry()
• nirs4all.core package
  • Subpackages
    • nirs4all.core.logging package
      • Submodules
  • Submodules
    • nirs4all.core.config module
    • nirs4all.core.exceptions module
    • nirs4all.core.metrics module
      • abbreviate_metric()
      • eval()
      • eval_list()
      • eval_multi()
      • get_available_metrics()
      • get_default_metrics()
      • get_stats()
    • nirs4all.core.task_detection module
      • detect_task_type()
    • nirs4all.core.task_type module
      • matches_task_type()
      • resolve_task_type_sql()
• nirs4all.data package
  • Subpackages
    • nirs4all.data.detection package
      • Submodules
    • nirs4all.data.loaders package
      • Submodules
    • nirs4all.data.parsers package
      • Submodules
    • nirs4all.data.performance package
      • Submodules
    • nirs4all.data.schema package
      • Subpackages
      • Submodules
    • nirs4all.data.selection package
      • Submodules
    • nirs4all.data.serialization package
      • Submodules
  • Submodules
    • nirs4all.data.binning module
    • nirs4all.data.config module
    • nirs4all.data.config_parser module
      • browse_folder()
      • folder_to_name()
    • nirs4all.data.dataset module
    • nirs4all.data.ensemble_utils module
    • nirs4all.data.features module
    • nirs4all.data.fit_influence module
      • FitInfluenceError
      • FitInfluenceMode
    • nirs4all.data.indexer module
    • nirs4all.data.meta_features module
      • AlignedMetaFeatures
      • MetaFeatureAlignmentError
      • PredictionFeatureVector
      • align_prediction_feature_vectors()
    • nirs4all.data.metadata module
    • nirs4all.data.multimodal module
      • MultimodalSpectroDataset
    • nirs4all.data.predictions module
      • MergeReport
      • PredictionResult
      • PredictionResultsList
    • nirs4all.data.raw_multisource module
      • AlignedMaterialization
      • CARTESIAN_REPRESENTATIONS
      • CombinationPlan
      • ComboSelection
      • DECLARED_REPRESENTATIONS
      • EXECUTABLE_REPRESENTATIONS
      • RawMultiSourceDataset
      • RepresentationPlan
      • RepresentationStage
      • RepresentationUnitLevel
      • replay_materialization()
    • nirs4all.data.reduction module
      • EvaluationScope
      • FitScope
      • LeakedReducerStateError
      • PSEUDO_FOLD_IDS
      • PredictionLevel
      • PredictionScope
      • PredictionUnitId
      • REFIT_FOLD_IDS
      • ReducerState
      • ReductionAxis
      • ReductionError
      • ReductionMethod
      • ReductionPlan
      • ReductionRole
      • TaskCompatibility
      • is_real_cv_fold()
      • normalize_evaluation_scope()
      • prediction_scope_from_legacy()
    • nirs4all.data.relation_replay_manifest module
      • RelationReplayManifest
      • RelationReplayManifestError
      • build_relation_replay_manifest()
    • nirs4all.data.relations module
      • ComboRecord
      • MissingRepetitionPolicy
      • MissingSourcePolicy
      • NormalizedObservationTable
      • ObservationRecord
      • Partition
      • QualityFlag
      • RELATION_TABLE_COLUMNS
      • REPETITION_MECHANISMS
      • RelationConfig
      • RelationValidationError
      • RepOrder
      • RepetitionSpec
      • SampleRelationPlan
      • SourceObservations
      • SourceRepetitionSpec
      • UnitLevel
      • audit_link_by_alignment()
      • audit_link_by_executable()
      • audit_source_lengths()
      • build_relation_table()
      • check_repetition_exclusivity()
      • detect_repetition_mechanisms()
      • make_observation_id()
      • parse_relation_config()
    • nirs4all.data.repetition_detection module
      • RepetitionGroups
    • nirs4all.data.signal_type module
      • SignalTypeDetector
    • nirs4all.data.targets module
    • nirs4all.data.types module
      • get_num_samples()
• nirs4all.operators package
  • Subpackages
    • nirs4all.operators.augmentation package
      • Submodules
    • nirs4all.operators.base package
      • Submodules
    • nirs4all.operators.data package
      • Submodules
    • nirs4all.operators.filters package
      • Submodules
    • nirs4all.operators.methods package
      • Submodules
    • nirs4all.operators.models package
      • Subpackages
      • Submodules
    • nirs4all.operators.splitters package
      • Submodules
    • nirs4all.operators.transforms package
      • Submodules
• nirs4all.optimization package
  • Submodules
    • nirs4all.optimization.n4m_engine module
      • N4MFinetuneManager
    • nirs4all.optimization.optuna module
      • BinarySearchSampler
      • stack_params()
    • nirs4all.optimization.preprocessing module
• nirs4all.pipeline package
  • Subpackages
    • nirs4all.pipeline.analysis package
      • Submodules
    • nirs4all.pipeline.bundle package
      • Submodules
    • nirs4all.pipeline.config package
      • Submodules
    • nirs4all.pipeline.dagml package
      • Submodules
    • nirs4all.pipeline.execution package
      • Subpackages
      • Submodules
    • nirs4all.pipeline.steps package
      • Submodules
    • nirs4all.pipeline.storage package
      • Subpackages
      • Submodules
    • nirs4all.pipeline.trace package
      • Submodules
  • Submodules
    • nirs4all.pipeline.dagml_bridge module
      • compile_with_dagml()
      • constrained_operator_survivor_sequences()
      • is_grid_param_generator_spec()
      • is_param_generator_spec()
      • lower_constrained_operator_pipeline()
      • operator_choice_variant_label()
      • operator_sequence_variant_label()
      • step_has_native_grid()
    • nirs4all.pipeline.engine module
      • ExecutionProfileError
      • LegacyEngineUsageWarning
      • get_legacy_engine_usage_counts()
      • legacy_fallback_metrics()
      • require_legacy_engine()
    • nirs4all.pipeline.explain_lineage module
      • RelationExplainLineage
    • nirs4all.pipeline.explainer module
      • Explainer
    • nirs4all.pipeline.keyword_registry module
      • get_keyword_registry()
      • get_keyword_registry_schema()
    • nirs4all.pipeline.minimal_predictor module
      • MinimalArtifactProvider
      • MinimalPredictor
    • nirs4all.pipeline.portable_n4m_roles module
      • PortableN4MRolePipeline
    • nirs4all.pipeline.portable_n4m_trained module
      • PortableN4MTrainedPipeline
      • RefittedN4MPipeline
    • nirs4all.pipeline.predictor module
      • Predictor
    • nirs4all.pipeline.resolver module
      • FoldStrategy
      • SourceType
    • nirs4all.pipeline.retrainer module
      • ExtractedPipeline
      • RetrainArtifactProvider
      • RetrainConfig
      • RetrainMode
      • Retrainer
      • StepMode
    • nirs4all.pipeline.run module
      • DatasetInfo
      • Run
      • RunConfig
      • RunStatus
      • RunSummary
      • TemplateInfo
      • generate_run_id()
      • get_metric_info()
      • is_better_score()
    • nirs4all.pipeline.runner module
      • init_global_random_state()
• nirs4all.sklearn package
  • Submodules
    • nirs4all.sklearn.classifier module
      • NIRSPipelineClassifier
    • nirs4all.sklearn.pipeline module
• nirs4all.synthesis package
  • Submodules
    • nirs4all.synthesis.accelerated module
      • AcceleratedArrays
      • AcceleratedGenerator
      • AcceleratorBackend
      • benchmark_backends()
      • create_accelerated_arrays()
      • detect_best_backend()
      • generate_spectra_batch_accelerated()
      • generate_voigt_profiles_accelerated()
      • get_acceleration_speedup_estimate()
      • get_backend_info()
      • is_gpu_available()
    • nirs4all.synthesis.benchmarks module
      • BenchmarkDatasetInfo
      • BenchmarkDomain
      • LoadedBenchmarkDataset
      • create_synthetic_matching_benchmark()
      • get_benchmark_info()
      • get_benchmark_spectral_properties()
      • get_datasets_by_domain()
      • list_benchmark_datasets()
      • load_benchmark_dataset()
    • nirs4all.synthesis.builder module
      • BuilderState
    • nirs4all.synthesis.components module
      • NIRBand
      • SpectralComponent
      • available_components()
      • component_info()
      • get_component()
      • list_categories()
      • normalize_component_amplitudes()
      • search_components()
      • validate_component_coverage()
      • validate_predefined_components()
    • nirs4all.synthesis.config module
    • nirs4all.synthesis.detectors module
      • DetectorConfig
      • DetectorSimulator
      • DetectorSpectralResponse
      • NoiseModelConfig
      • get_default_noise_config()
      • get_detector_response()
      • get_detector_wavelength_range()
      • list_detector_types()
      • simulate_detector_effects()
    • nirs4all.synthesis.domains module
      • ConcentrationPrior
      • DomainCategory
      • DomainConfig
      • create_domain_aware_library()
      • get_domain_components()
      • get_domain_config()
      • get_domains_for_component()
      • list_domains()
    • nirs4all.synthesis.environmental module
      • EnvironmentalEffectsConfig
      • MoistureConfig
      • SpectralRegion
      • TemperatureConfig
      • TemperatureEffectParams
      • get_temperature_effect_regions()
    • nirs4all.synthesis.exporter module
      • CSVVariationGenerator
      • DatasetExporter
      • ExportConfig
      • export_to_csv()
      • export_to_folder()
    • nirs4all.synthesis.fitter module
      • ComponentFitResult
      • ComponentFitter
      • DerivativeAwareForwardModelFitter
      • DomainInference
      • EdgeArtifactInference
      • EnvironmentalInference
      • FittedParameters
      • ForwardModelFitter
      • InstrumentChain
      • InstrumentInference
      • MeasurementModeInference
      • OperatorVarianceParams
      • OptimizedComponentFitter
      • OptimizedFitResult
      • PCAVarianceParams
      • PreprocessingInference
      • PreprocessingType
      • RealBandFitResult
      • RealBandFitter
      • RealDataFitter
      • ScatteringInference
      • SpectralProperties
      • VarianceFitResult
      • VarianceFitter
      • compare_datasets()
      • compute_spectral_properties()
      • fit_components()
      • fit_components_optimized()
      • fit_real_bands()
      • fit_to_real_data()
      • fit_variance()
      • multiscale_derivative_fit()
      • multiscale_fit()
    • nirs4all.synthesis.generator module
    • nirs4all.synthesis.instruments module
      • DetectorType
      • InstrumentCategory
      • MonochromatorType
      • get_instrument_wavelength_info()
      • get_instruments_by_category()
      • list_instrument_archetypes()
      • list_instrument_wavelength_grids()
    • nirs4all.synthesis.measurement_modes module
      • ATRConfig
      • ReflectanceConfig
      • ScatteringConfig
      • TransflectanceConfig
      • TransmittanceConfig
      • create_atr_simulator()
      • create_reflectance_simulator()
      • create_transmittance_simulator()
    • nirs4all.synthesis.metadata module
      • generate_sample_metadata()
    • nirs4all.synthesis.prior module
      • MatrixType
      • NIRSPriorConfig
      • PriorSampler
      • get_domain_compatible_instruments()
      • get_instrument_typical_modes()
      • sample_prior()
      • sample_prior_batch()
    • nirs4all.synthesis.procedural module
      • FunctionalGroupType
      • ProceduralComponentConfig
      • ProceduralComponentGenerator
    • nirs4all.synthesis.products module
      • CategoryGenerator
      • ComponentVariation
      • ProductGenerator
      • ProductTemplate
      • VariationType
      • generate_product_samples()
      • get_product_template()
      • list_product_categories()
      • list_product_domains()
      • list_product_templates()
      • product_template_info()
    • nirs4all.synthesis.scattering module
      • ParticleSizeDistribution
      • ScatteringCoefficientConfig
      • ScatteringModel
    • nirs4all.synthesis.sources module
      • MultiSourceGenerator
      • MultiSourceResult
      • SourceConfig
      • generate_multi_source()
    • nirs4all.synthesis.targets module
      • ClassSeparationConfig
      • generate_classification_targets()
      • generate_regression_targets()
    • nirs4all.synthesis.validation module
      • DatasetComparisonResult
      • MetricResult
      • RealismMetric
      • SpectralRealismScore
      • ValidationError
      • compute_adversarial_validation_auc()
      • compute_baseline_curvature()
      • compute_correlation_length()
      • compute_derivative_statistics()
      • compute_distribution_overlap()
      • compute_peak_density()
      • compute_snr()
      • compute_spectral_realism_scorecard()
      • quick_realism_check()
      • validate_against_benchmark()
      • validate_concentrations()
      • validate_spectra()
      • validate_synthetic_output()
      • validate_wavelengths()
    • nirs4all.synthesis.wavenumber module
      • CombinationBandResult
      • OvertoneResult
      • apply_hydrogen_bonding_shift()
      • calculate_combination_band()
      • calculate_overtone_position()
      • classify_wavelength_extended()
      • classify_wavelength_zone()
      • convert_bandwidth_to_wavelength()
      • convert_bandwidth_to_wavenumber()
      • estimate_bandwidth_broadening()
      • get_all_zones_extended()
      • get_all_zones_wavelength()
      • get_nir_overtones_for_fundamental()
      • get_zone_wavelength_range()
      • is_nir_region()
      • is_visible_region()
      • wavelength_to_wavenumber()
      • wavenumber_to_wavelength()
• nirs4all.utils package
  • Submodules
    • nirs4all.utils.backend module
      • clear_availability_cache()
      • get_backend_info()
      • get_gpu_info()
      • is_ikpls_available()
      • is_jax_available()
      • is_keras_available()
      • is_tensorflow_available()
      • is_torch_available()
      • lazy_import()
      • print_backend_status()
    • nirs4all.utils.hashing module
      • compute_data_hash()
    • nirs4all.utils.header_units module
      • parse_numeric_headers()
      • should_invert_x_axis()
    • nirs4all.utils.lazy module
      • LazyModule
    • nirs4all.utils.memory module
      • estimate_cache_entry_bytes()
      • estimate_dataset_bytes()
      • format_bytes()
      • get_process_rss_mb()
    • nirs4all.utils.operator_formatting module
      • format_operator_with_params()
    • nirs4all.utils.spinner module
      • Spinner
      • spinner_context()
    • nirs4all.utils.transform_output module
• nirs4all.visualization package
  • Subpackages
    • nirs4all.visualization.analysis package
      • Submodules
    • nirs4all.visualization.chart_utils package
      • Submodules
    • nirs4all.visualization.charts package
      • Submodules
  • Submodules
    • nirs4all.visualization.display module
      • finalize_figures()
      • has_interactive_display()
      • normalize_figures()
    • nirs4all.visualization.naming module
    • nirs4all.visualization.pipeline_diagram module
      • PipelineDiagram
      • PipelineNode
      • plot_pipeline_diagram()
    • nirs4all.visualization.prediction_cache module
      • CacheKey
      • PredictionCache
    • nirs4all.visualization.predictions module
      • PredictionAnalyzer
    • nirs4all.visualization.reports module
• nirs4all.workspace package
  • Submodules
    • nirs4all.workspace.compat module
      • ConversionRequired
      • WorkspaceFormatInfo
      • build_conversion_command()
      • default_conversion_output()
      • inspect_workspace_format()
      • warn_if_legacy_workspace()
    • nirs4all.workspace.upgrade module
      • upgrade_workspace_copy()

Submodules

• nirs4all.runtime module
  • from_native_dir()
  • list_controller_manifests()